visualiseHybridisations      package:arrayMagic      R Documentation

_M_i_c_r_o_a_r_r_a_y _i_n_t_e_n_s_i_t_y _d_a_t_a _a_r_e _v_i_s_u_a_l_i_s_e_d _w_i_t_h _r_e_s_p_e_c_t
_t_o _t_h_e_i_r _s_p_a_t_i_a_l _l_a_y_o_u_t

_D_e_s_c_r_i_p_t_i_o_n:

     Two colour microarray intensity data are visualised with respect
     to their spatial layout. Missing values ('NA') as well as minus
     infinity ('-Inf') etc. are not visualised. They appear to be
     white, i.e. in the colour of the background. '-Inf' might be a
     result of the (log-)transformation of the data; cf. the argument
     'transFunc'.

_U_s_a_g_e:

     visualiseHybridisations(arrayDataObject, exprSetRGObject, type="raw", hybridisations, slideNameColumn, numberOfSpots, nrOfBlocksPerRow=4, mappingColumns= list(Block="Block", Column="Column", Row="Row"), transFunc=log, savePath=".", plotOutput="pdf")

_A_r_g_u_m_e_n_t_s:

arrayDataObject: object of class 'arrayData'; required; default:
          missing

exprSetRGObject: object of class 'exprSetRG'; only required, if 'type =
          "normalised"' or 'type = "normalisedLogRatio"'; default:
          missing

    type: vector of character strings; required; default "raw"; valid
          strings are "raw", "rawLogRatio",
          "rawLogRatioBackgroundSubtracted", "normalised" or
          "normalisedLogRatio"

hybridisations: vector of integers; optional; default: missing, i.e.
          all microarray slides

slideNameColumn: character string specifying the column
          'getHybAttr(arrayDataObject)' which contains the names of the
          hybridisations; optional; default: missing

numberOfSpots: integer; optional; default: missing; but required if the
          values in 'arrayDataObject' do not cover the whole microarray
          slide, i.e. do not contain all spots; cf. 'spatialLayout'.

nrOfBlocksPerRow: integer; cf. 'spatialLayout'; required; default: 4

mappingColumns: list; required; the list elements named "Block",
          "Column", "Row" define the corresponding column names given
          in 'getSpotAttr(arrayDataObject)'; the "Block" element is
          optional, if missing a single block is assumed; default:
          'list(Block="Block", Column="Column", Row="Row")'; cf.
          'spatialLayout' 

transFunc: transformation function applied to the raw data, in
          particular in combination with 'type = "raw"' you may for
          example use 'log' or 'rank'; (note: 'type = "rawLogRatio"'
          and 'type = "rawLogRatioBackgroundSubtracted"' require log );
          required; default: log

savePath: character string; required; default: "."

plotOutput: character string; required; either "screen", "pdf" or
          "win.metafile"; default: "pdf"

_V_a_l_u_e:

     None, but a plot is generated.

_A_u_t_h_o_r(_s):

     Andreas Buness <a.buness@dkfz.de>

_S_e_e _A_l_s_o:

     'spatialLayout', 'exprSetRG-class', 'arrayData-class'

_E_x_a_m_p_l_e_s:

             

